DNA-Methylation and Alternative Splicing

Question

[sc@791]

Hello Everyone,

I want to plot DNA methylation around splice sites (5’ SS and 3’ SS) or simply around splice junctions. I have bigwig and .tsv files for methylome data generated using the methylpy program. The header of these files looks like:

1              34           -              CAG       4              11           1
1              76           +             CCA        0              1              1
1              77           +             CAT        1              1              1
1              80           -              CAT        5              41           1
1              84           +             CCC        0              3              1
1              85           +             CCT        2              4              1
1              86           +             CTA        2              4              1
1              93           +             CCT        1              4              1
1              94           +             CTA        2              4              1
1              100         +             CCC        2              5              1

On the other hand, I have splice sites files as .tsv format generated from RNA-Seq data using HISAT2. The header of these files looks like:

1              3912       3995       +
1              4275       4485       +
1              4604       4705       +
1              5094       5173       +
1              5325       5438       +
1              7068       7156       -
1              7231       7383       -
1              7250       7383       -
1              7449       7563       -
1              7648       7761       -

The reference genome is Arabidopsis. Now I want to compare these two data and plot methylation pattern around the splice sites. It would be great if you provide any suggestions or recommendation for this analysis.

Any help is much appreciated

Thank you

Regards

Saurabh